Alice Barkan

Summary

Affiliation: University of Oregon
Country: USA

Publications

  1. ncbi request reprint Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins
    Gerard J Ostheimer
    Institute of Molecular Biology, 1229 University of Oregon, Eugene, OR 97403, USA
    Structure 10:1593-601. 2002
  2. pmc CRS1, a chloroplast group II intron splicing factor, promotes intron folding through specific interactions with two intron domains
    Oren Ostersetzer
    Department of Biology and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Plant Cell 17:241-55. 2005
  3. pmc The maize tha4 gene functions in sec-independent protein transport in chloroplasts and is related to hcf106, tatA, and tatB
    M B Walker
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    J Cell Biol 147:267-76. 1999
  4. doi request reprint Studying the structure and processing of chloroplast transcripts
    Alice Barkan
    Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
    Methods Mol Biol 774:183-97. 2011
  5. pmc The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein
    Alice Barkan
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403 1229, USA
    RNA 13:55-64. 2007
  6. ncbi request reprint Formation of the CRS2-CAF2 group II intron splicing complex is mediated by a 22-amino acid motif in the COOH-terminal region of CAF2
    Gerard J Ostheimer
    Institute of Molecular Biology, Department of Chemistry and Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
    J Biol Chem 281:4732-8. 2006
  7. pmc A ribonuclease III domain protein functions in group II intron splicing in maize chloroplasts
    Kenneth P Watkins
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Plant Cell 19:2606-23. 2007
  8. pmc A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis
    Jana Prikryl
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97405, USA
    Nucleic Acids Res 36:5152-65. 2008
  9. pmc A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts
    Yukari Asakura
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Plant Cell 19:3864-75. 2007
  10. pmc APO1 promotes the splicing of chloroplast group II introns and harbors a plant-specific zinc-dependent RNA binding domain
    Kenneth P Watkins
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Plant Cell 23:1082-92. 2011

Collaborators

  • Christian Schmitz-Linneweber
  • Brian W Matthews
  • Ian Small
  • Kamel Hammani
  • David B Stern
  • Lalit Ponnala
  • Kenneth P Watkins
  • Yukari Asakura
  • Rosalind Williams-Carrier
  • Gerard J Ostheimer
  • Giulia Friso
  • Klaas J van Wijk
  • Jana Prikryl
  • Susan Belcher
  • Reimo Zoschke
  • Tiffany Kroeger
  • Margarita Rojas
  • Tiffany S Kroeger
  • Anastassia Khrouchtchova
  • Petya Zhelyazkova
  • Wojciech Majeran
  • Dylan B Udy
  • Catherine Colas des Francs-Small
  • Rita Ann Monde
  • Jeannette Pfalz
  • Nicholas Stiffler
  • Omer Ali Bayraktar
  • Susanne Beick
  • Nigel S Walker
  • Amy M Cooke
  • Haralambos Hadjivassiliou
  • Oren Ostersetzer
  • Erin Osborne
  • Pascale M Williams
  • Oren Ostersetzer-Biran
  • Mark Aurel Schöttler
  • Rodger Voelker
  • Xian Qu
  • Jose M Gualberto
  • Mingshu Huang
  • Thomas Börner
  • Michal Zmudjak
  • Martín Vargas-Suárez
  • Nima Rahimi
  • Gadi Schuster
  • Jorg Meurer
  • Robert Coalter
  • Bryan Jensen
  • M B Walker
  • Rosalind E Williams-Carrier
  • Susan E Belcher
  • Haralambos Hadjivasiliou
  • Daniel P Kloer
  • Toshiya Hirohashi
  • Masato Nakai
  • Ichiro Terashima
  • Shingo Kikuchi
  • Satoshi Yano
  • Jennifer Gierke
  • L M Roy
  • E Coleman
  • R Voelker

Detail Information

Publications36

  1. ncbi request reprint Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins
    Gerard J Ostheimer
    Institute of Molecular Biology, 1229 University of Oregon, Eugene, OR 97403, USA
    Structure 10:1593-601. 2002
    ..Taken together, the evidence suggests that members of UPF0044 constitute a previously unrecognized class of RNA binding domain...
  2. pmc CRS1, a chloroplast group II intron splicing factor, promotes intron folding through specific interactions with two intron domains
    Oren Ostersetzer
    Department of Biology and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Plant Cell 17:241-55. 2005
    ..We conclude that CRS1 promotes the folding of its group II intron target through tight and specific interactions with two peripheral intron segments...
  3. pmc The maize tha4 gene functions in sec-independent protein transport in chloroplasts and is related to hcf106, tatA, and tatB
    M B Walker
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    J Cell Biol 147:267-76. 1999
    ..These findings support the notion that this sec-independent translocation mechanism has been highly conserved during the evolution of eucaryotic organelles from bacterial endosymbionts...
  4. doi request reprint Studying the structure and processing of chloroplast transcripts
    Alice Barkan
    Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
    Methods Mol Biol 774:183-97. 2011
    ..A protocol is provided for a poisoned-primer extension assay for quantifying different splice isoforms...
  5. pmc The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein
    Alice Barkan
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403 1229, USA
    RNA 13:55-64. 2007
    ....
  6. ncbi request reprint Formation of the CRS2-CAF2 group II intron splicing complex is mediated by a 22-amino acid motif in the COOH-terminal region of CAF2
    Gerard J Ostheimer
    Institute of Molecular Biology, Department of Chemistry and Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
    J Biol Chem 281:4732-8. 2006
    ..We propose that this surface binds the hydrophobic patch on the surface of CRS2 previously shown to be necessary for the interaction between CRS2 and CAF2...
  7. pmc A ribonuclease III domain protein functions in group II intron splicing in maize chloroplasts
    Kenneth P Watkins
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Plant Cell 19:2606-23. 2007
    ..These results suggest that RNC1 is recruited to specific introns via protein-protein interactions and that its role in splicing involves RNA binding but not RNA cleavage activity...
  8. pmc A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis
    Jana Prikryl
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97405, USA
    Nucleic Acids Res 36:5152-65. 2008
    ..However, these mutants contain near normal levels of chloroplast DNA and RNAs, suggesting that ZmWHY1 is not directly required for either DNA replication or for global plastid transcription...
  9. pmc A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts
    Yukari Asakura
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Plant Cell 19:3864-75. 2007
    ..With these findings, CRM domain proteins are implicated in the activities of three classes of catalytic RNA: group I introns, group II introns, and 23S rRNA...
  10. pmc APO1 promotes the splicing of chloroplast group II introns and harbors a plant-specific zinc-dependent RNA binding domain
    Kenneth P Watkins
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Plant Cell 23:1082-92. 2011
    ..Thus, DUF794 adds a new example to the repertoire of plant-specific RNA binding domains that emerged as a product of nuclear-organellar coevolution...
  11. doi request reprint Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize
    Rosalind Williams-Carrier
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
    Plant J 63:167-77. 2010
    ..A by-product of the approach is the identification of numerous heritable insertions that are unrelated to the targeted phenotype, which can contribute to community insertion resources...
  12. pmc A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing
    Tiffany S Kroeger
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
    Proc Natl Acad Sci U S A 106:4537-42. 2009
    ..These findings add to emerging evidence that the coevolution of nuclear and organellar genomes spurred the evolution of diverse noncanonical RNA-binding motifs that perform organelle-specific functions...
  13. pmc A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins
    Alice Barkan
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
    PLoS Genet 8:e1002910. 2012
    ..Furthermore, the extraordinary evolutionary plasticity of the PPR family suggests that the PPR scaffold will be particularly amenable to redesign for new sequence specificities and functions...
  14. pmc Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein
    Jana Prikryl
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
    Proc Natl Acad Sci U S A 108:415-20. 2011
    ....
  15. pmc Sequence-specific binding of a chloroplast pentatricopeptide repeat protein to its native group II intron ligand
    Rosalind Williams-Carrier
    Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    RNA 14:1930-41. 2008
    ..These results suggest mechanisms by which PPR5 influences both RNA stability and splicing...
  16. ncbi request reprint Structural analysis of the group II intron splicing factor CRS2 yields insights into its protein and RNA interaction surfaces
    Gerard J Ostheimer
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
    J Mol Biol 345:51-68. 2005
    ..Both the sequence and the structural context of the amino acid residues essential for peptidyl-tRNA hydrolase activity are conserved in CRS2, yet expression of CRS2 is incapable of rescuing a pth(ts)E.coli strain...
  17. pmc RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression
    Kamel Hammani
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
    Proc Natl Acad Sci U S A 109:5651-6. 2012
    ..We suggest that analogous activities contribute to the functions of HAT domains found in ribonucleoprotein complexes in the nuclear-cytosolic compartment...
  18. pmc Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts
    Yukari Asakura
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
    RNA 14:2319-32. 2008
    ....
  19. pmc A short PPR protein required for the splicing of specific group II introns in angiosperm chloroplasts
    Anastassia Khrouchtchova
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    RNA 18:1197-209. 2012
    ..THA8 is the first member of this subfamily with a defined molecular function, and illustrates that even small PPR proteins have the potential to mediate specific intermolecular interactions in vivo...
  20. pmc Protein-mediated protection as the predominant mechanism for defining processed mRNA termini in land plant chloroplasts
    Petya Zhelyazkova
    Institute for Biology Genetics, Humboldt University Berlin, D 10115 Berlin, Germany
    Nucleic Acids Res 40:3092-105. 2012
    ..We show that most processed mRNA termini are represented by small RNAs whose sequences are highly conserved. We suggest that each such small RNA is the footprint of a PPR-like protein that protects the adjacent RNA from degradation...
  21. pmc A pentatricopeptide repeat protein facilitates the trans-splicing of the maize chloroplast rps12 pre-mRNA
    Christian Schmitz-Linneweber
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Plant Cell 18:2650-63. 2006
    ..These findings add trans-splicing to the list of RNA-related functions associated with PPR proteins and suggest that plastid group II trans-splicing is performed by different machineries in vascular plants and algae...
  22. doi request reprint Genome-wide analysis of RNA-protein interactions in plants
    Alice Barkan
    Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
    Methods Mol Biol 553:13-37. 2009
    ..This chapter reviews approaches for defining the native RNA ligands of RBPs on a genome-wide scale and provides a protocol for a method that has been used to this end for RBPs that localize to the chloroplast...
  23. pmc Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns
    Yukari Asakura
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Plant Physiol 142:1656-63. 2006
    ..Finally, we show that a strong AtCAF2 allele conditions an embryo-lethal phenotype, adding to the body of data suggesting that cell viability is more sensitive to the loss of plastid translation in Arabidopsis than in maize...
  24. pmc Group II intron splicing factors derived by diversification of an ancient RNA-binding domain
    Gerard J Ostheimer
    Institute of Molecular Biology, Department of Chemistry, University of Oregon, Eugene, OR 97403, USA
    EMBO J 22:3919-29. 2003
    ..We propose that the CRM domain is an ancient RNA-binding module that has diversified to mediate specific interactions with various highly structured RNAs...
  25. pmc POGs/PlantRBP: a resource for comparative genomics in plants
    Nigel S Walker
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
    Nucleic Acids Res 35:D852-6. 2007
    ....
  26. ncbi request reprint A chloroplast-localized PPR protein required for plastid ribosome accumulation
    Pascale M Williams
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
    Plant J 36:675-86. 2003
    ..Taken together, the results suggest that ppr2 functions in the synthesis or assembly of one or more component of the plastid translation machinery...
  27. pmc Site-specific binding of a PPR protein defines and stabilizes 5' and 3' mRNA termini in chloroplasts
    Jeannette Pfalz
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
    EMBO J 28:2042-52. 2009
    ..These results, together with recent insights into bacterial RNA decay, suggest a unifying model for the biogenesis of chloroplast transcript populations and for the determinants of chloroplast mRNA stability...
  28. pmc RNA immunoprecipitation and microarray analysis show a chloroplast Pentatricopeptide repeat protein to be associated with the 5' region of mRNAs whose translation it activates
    Christian Schmitz-Linneweber
    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
    Plant Cell 17:2791-804. 2005
    ..Analogous methods should have broad application for the study of native RNA-protein interactions in both mitochondria and chloroplasts...
  29. pmc Effects of reduced chloroplast gene copy number on chloroplast gene expression in maize
    Dylan B Udy
    Department of Biology and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Plant Physiol 160:1420-31. 2012
    ..Mitochondrial DNA copy number was reduced approximately 2-fold in mutants harboring strong w2 alleles, suggesting that w2 also contributes to mitochondrial DNA replication...
  30. pmc Nucleoid-enriched proteomes in developing plastids and chloroplasts from maize leaves: a new conceptual framework for nucleoid functions
    Wojciech Majeran
    Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA
    Plant Physiol 158:156-89. 2012
    ..Details of protein identification and annotation are provided in the Plant Proteome Database...
  31. doi request reprint The pentatricopeptide repeat-SMR protein ATP4 promotes translation of the chloroplast atpB/E mRNA
    Reimo Zoschke
    Molekulare Genetik, Institut fur Biologie, Humboldt Universitat zu Berlin, D 10115 Berlin, Germany
    Plant J 72:547-58. 2012
    ..ATP4 is orthologous to the Arabidopsis protein SVR7, but the phenotypes of atp4 and svr7 mutants suggest that the functions of these orthologs have not been strictly conserved...
  32. pmc A rapid ribosome profiling method elucidates chloroplast ribosome behavior in vivo
    Reimo Zoschke
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
    Plant Cell 25:2265-75. 2013
    ..An analogous approach is likely to be useful for studies of mitochondrial gene expression. ..
  33. doi request reprint A PORR domain protein required for rpl2 and ccmF(C) intron splicing and for the biogenesis of c-type cytochromes in Arabidopsis mitochondria
    Catherine Colas des Francs-Small
    Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009 WA, Australia
    Plant J 69:996-1005. 2012
    ....
  34. pmc Maize mutants lacking chloroplast FtsY exhibit pleiotropic defects in the biogenesis of thylakoid membranes
    Yukari Asakura
    Institute for Protein Research, Osaka University, Suita, Osaka 565 0871, Japan
    Plant Cell 16:201-14. 2004
    ..These results demonstrate the essentiality of cpFtsY for the biogenesis not only of the LHCPs but also for the assembly of the other membrane-bound components of the photosynthetic apparatus...
  35. pmc The pentatricopeptide repeat protein PPR5 stabilizes a specific tRNA precursor in maize chloroplasts
    Susanne Beick
    Humboldt University Berlin, Institute of Biology, Chausseestr 117, 10115 Berlin, Germany
    Mol Cell Biol 28:5337-47. 2008
    ..These findings add to the evidence that chloroplast-localized PPR proteins that are embryo essential in Arabidopsis typically function in the biogenesis of the plastid translation machinery...
  36. ncbi request reprint Genetics and genomics of chloroplast biogenesis: maize as a model system
    David B Stern
    Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
    Trends Plant Sci 9:293-301. 2004